Abstract Secreted and cell-surface-localized Immunoglobulin Superfamily proteins (`extracellular IgSFs') are important class of proteins, which includes proven targets for the treatment of autoimmune diseases and cancer. The human proteome contains ~500 extracellular IgSFs, the largest superfamily of cell surface molecules that contribute to the regulation of innate and adaptive immunity, via specific IgSF:IgSF interactions at the `Immunological Synapse? formed between antigen-presenting cells and T-cells. Our long-term goal is to understand the principles underlying molecular recognition and selectivity at the immunological synapse through a multi-disciplinary program exploiting complementary computational and experimental approaches. These studies are essential to (i) understand the molecular basis of normal immune function associated with IgSFs; (ii) define the mechanisms underlying IgSF-associated dysfunction and disease, and (iii) define strategies to re-engineer IgSF receptor:ligand interactions for the realization of surgically defined mutants with altered affinities and selectivities, which can act as biologic drugs (as demonstrated by FDA-approved biologics for some of these targets such as Orencia? and Belatacept). Our goal in this application is (1) to identify the protein-protein binding sites specific for individual IgSF members; here, we will exploit our previously published approaches that combine structure and sequence information that identified functional subfamilies of the IgSF. We also present a new approach that identifies binding sites by their physico-chemical and spatial ?uniqueness? (2) Develop a protein design-aided pharmacophore approach to identify cognate receptor-ligand pairs of IgSFs; We present a new method that exploits the ligand-based pharmacophore drug design concept, where we characterize the receptor:ligand interface by a unique spatial fingerprint of energetically favorable `residue-specific-pharmacophores'. However, instead of ligand binding information here we use preferences of amino acid residues or residue fragments that are obtained from molecular dynamics simulations. (3) Experimentally verify predicted receptor-ligand partners and explore binding specificity of mutants. Our project will directly expand the current knowledgebase of IgSF:IgSF binding pairs and yield mutant molecules, with altered affinities and selectivities, for therapeutic applications. Our project will also deliver a protein-ligand screening tool applicable to other protein classes, and a novel `uniqueness'-driven hot-spot detection method for mutant design.